PDB Entry (2xd5) |
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PDB ID: 2xd5 | Resolution: 2.5 Å | Exp. Method: X-RAY DIFFRACTION |
PMID: - | DOI: - | |
Protein |
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Protein Name: DD-transpeptidase | |
Uniprot ID/ACC: Q7CRA4 (Q7CRA4_STRR6) | Organism: Streptococcus pneumoniae (strain ATCC BAA-255 / R6) |
Gene Symbol: pbp1b | Gene ID: - |
Protein Class: TRANSFERASE |
Ligand |
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Ligand Name: N-BENZOYL-D-ALANINE | ||
Canonical SMILES: C[C@@H](NC(=O)c1ccccc1)C(O)=O | ||
Standard InChI: InChI=1S/C10H11NO3/c1-7(10(13)14)11-9(12)8-5-3-2-4-6-8/h2-7H,1H3,(H,11,12)(H,13,14)/t7-/m1/s1 | ||
HET Code: S2D | PubChem: 91514 | |
DrugBank: DB08508 | ChEMBL: CHEMBL55771 | |
Molecular Formula: C10H11NO3 | Mol. Weight: 193.0739 | logP: 0.8895 |
HBD: 2 | HBA: 2 | |
#Rotatable Bonds: 3 | TPSA: 66.4 |
Covalent Mechanism |
Reaction Name | Residue | Chain ID | SASA | pKa | Warhead Name | Warhead Structure |
Nucleophilic Acyl Substitution | SER 460 | B | 12.86 | - | Carboxylic Acid |
Binding Affinity |
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